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 Ontologies


Bio-KGvec2go: Serving up-to-date Dynamic Biomedical Knowledge Graph Embeddings

arXiv.org Artificial Intelligence

Knowledge graphs and ontologies represent entities and their relationships in a structured way, having gained significance in the development of modern AI applications. Integrating these semantic resources with machine learning models often relies on knowledge graph embedding models to transform graph data into numerical representations. Therefore, pre-trained models for popular knowledge graphs and ontologies are increasingly valuable, as they spare the need to retrain models for different tasks using the same data, thereby helping to democratize AI development and enabling sustainable computing. In this paper, we present Bio-KGvec2go, an extension of the KGvec2go Web API, designed to generate and serve knowledge graph embeddings for widely used biomedical ontologies. Given the dynamic nature of these ontologies, Bio-KGvec2go also supports regular updates aligned with ontology version releases. By offering up-to-date embeddings with minimal computational effort required from users, Bio-KGvec2go facilitates efficient and timely biomedical research.


Automated Hierarchical Graph Construction for Multi-source Electronic Health Records

arXiv.org Machine Learning

Electronic Health Records (EHRs), comprising diverse clinical data such as diagnoses, medications, and laboratory results, hold great promise for translational research. EHR-derived data have advanced disease prevention, improved clinical trial recruitment, and generated real-world evidence. Synthesizing EHRs across institutions enables large-scale, generalizable studies that capture rare diseases and population diversity, but remains hindered by the heterogeneity of medical codes, institution-specific terminologies, and the absence of standardized data structures. These barriers limit the interpretability, comparability, and scalability of EHR-based analyses, underscoring the need for robust methods to harmonize and extract meaningful insights from distributed, heterogeneous data. To address this, we propose MASH (Multi-source Automated Structured Hierarchy), a fully automated framework that aligns medical codes across institutions using neural optimal transport and constructs hierarchical graphs with learned hyperbolic embeddings. During training, MASH integrates information from pre-trained language models, co-occurrence patterns, textual descriptions, and supervised labels to capture semantic and hierarchical relationships among medical concepts more effectively. Applied to real-world EHR data, including diagnosis, medication, and laboratory codes, MASH produces interpretable hierarchical graphs that facilitate the navigation and understanding of heterogeneous clinical data. Notably, it generates the first automated hierarchies for unstructured local laboratory codes, establishing foundational references for downstream applications.


Neuro-Symbolic AI for Cybersecurity: State of the Art, Challenges, and Opportunities

arXiv.org Artificial Intelligence

Traditional Artificial Intelligence (AI) approaches in cybersecurity exhibit fundamental limitations: inadequate conceptual grounding leading to non-robustness against novel attacks; limited instructibility impeding analyst-guided adaptation; and misalignment with cybersecurity objectives. Neuro-Symbolic (NeSy) AI has emerged with the potential to revolutionize cybersecurity AI. However, there is no systematic understanding of this emerging approach. These hybrid systems address critical cybersecurity challenges by combining neural pattern recognition with symbolic reasoning, enabling enhanced threat understanding while introducing concerning autonomous offensive capabilities that reshape threat landscapes. In this survey, we systematically characterize this field by analyzing 127 publications spanning 2019-July 2025. We introduce a Grounding-Instructibility-Alignment (G-I-A) framework to evaluate these systems, focusing on both cyber defense and cyber offense across network security, malware analysis, and cyber operations. Our analysis shows advantages of multi-agent NeSy architectures and identifies critical implementation challenges including standardization gaps, computational complexity, and human-AI collaboration requirements that constrain deployment. We show that causal reasoning integration is the most transformative advancement, enabling proactive defense beyond correlation-based approaches. Our findings highlight dual-use implications where autonomous systems demonstrate substantial capabilities in zero-day exploitation while achieving significant cost reductions, altering threat dynamics. We provide insights and future research directions, emphasizing the urgent need for community-driven standardization frameworks and responsible development practices that ensure advancement serves defensive cybersecurity objectives while maintaining societal alignment.


Towards Ontology-Based Descriptions of Conversations with Qualitatively-Defined Concepts

arXiv.org Artificial Intelligence

The controllability of Large Language Models (LLMs) when used as conversational agents is a key challenge, particularly to ensure predictable and user-personalized responses. This work proposes an ontology-based approach to formally define conversational features that are typically qualitative in nature. By leveraging a set of linguistic descriptors, we derive quantitative definitions for qualitatively-defined concepts, enabling their integration into an ontology for reasoning and consistency checking. We apply this framework to the task of proficiency-level control in conversations, using CEFR language proficiency levels as a case study. These definitions are then formalized in description logic and incorporated into an ontology, which guides controlled text generation of an LLM through fine-tuning. Experimental results demonstrate that our approach provides consistent and explainable proficiency-level definitions, improving transparency in conversational AI.


ODKE+: Ontology-Guided Open-Domain Knowledge Extraction with LLMs

arXiv.org Artificial Intelligence

Knowledge graphs (KGs) are foundational to many AI applications, but maintaining their freshness and completeness remains costly. We present ODKE+, a production-grade system that automatically extracts and ingests millions of open-domain facts from web sources with high precision. ODKE+ combines modular components into a scalable pipeline: (1) the Extraction Initiator detects missing or stale facts, (2) the Evidence Retriever collects supporting documents, (3) hybrid Knowledge Extractors apply both pattern-based rules and ontology-guided prompting for large language models (LLMs), (4) a lightweight Grounder validates extracted facts using a second LLM, and (5) the Corroborator ranks and normalizes candidate facts for ingestion. ODKE+ dynamically generates ontology snippets tailored to each entity type to align extractions with schema constraints, enabling scalable, type-consistent fact extraction across 195 predicates. The system supports batch and streaming modes, processing over 9 million Wikipedia pages and ingesting 19 million high-confidence facts with 98.8% precision. ODKE+ significantly improves coverage over traditional methods, achieving up to 48% overlap with third-party KGs and reducing update lag by 50 days on average. Our deployment demonstrates that LLM-based extraction, grounded in ontological structure and verification workflows, can deliver trustworthiness, production-scale knowledge ingestion with broad real-world applicability. A recording of the system demonstration is included with the submission and is also available at https://youtu.be/UcnE3_GsTWs.


Ontology-Aligned Embeddings for Data-Driven Labour Market Analytics

arXiv.org Artificial Intelligence

The limited ability to reason across occupational data from different sources is a long-standing bottleneck for data-driven labour market analytics. Previous research has relied on hand-crafted ontologies that allow such reasoning but are computationally expensive and require careful maintenance by human experts. The rise of language processing machine learning models offers a scalable alternative by learning shared semantic spaces that bridge diverse occupational vocabularies without extensive human curation. We present an embedding-based alignment process that links any free-form German job title to two established ontologies - the German Klassifikation der Berufe and the International Standard Classification of Education. Using publicly available data from the German Federal Employment Agency, we construct a dataset to fine-tune a Sentence-BERT model to learn the structure imposed by the ontologies. The enriched pairs (job title, embedding) define a similarity graph structure that we can use for efficient approximate nearest-neighbour search, allowing us to frame the classification process as a semantic search problem. This allows for greater flexibility, e.g., adding more classes. We discuss design decisions, open challenges, and outline ongoing work on extending the graph with other ontologies and multilingual titles.


Towards an Action-Centric Ontology for Cooking Procedures Using Temporal Graphs

arXiv.org Artificial Intelligence

Formalizing cooking procedures remains a challenging task due to their inherent complexity and ambiguity. We introduce an extensible domain-specific language for representing recipes as directed action graphs, capturing processes, transfers, environments, concurrency, and compositional structure. Our approach enables precise, modular modeling of complex culinary workflows. Initial manual evaluation on a full English breakfast recipe demonstrates the DSL's expressiveness and suitability for future automated recipe analysis and execution. This work represents initial steps towards an action-centric ontology for cooking, using temporal graphs to enable structured machine understanding, precise interpretation, and scalable automation of culinary processes - both in home kitchens and professional culinary settings.


Extending FKG.in: Towards a Food Claim Traceability Network

arXiv.org Artificial Intelligence

The global food landscape is rife with scientific, cultural, and commercial claims about what foods are, what they do, what they should not do, or should not do. These range from rigorously studied health benefits (probiotics improve gut health) and misrepresentations (soaked almonds make one smarter) to vague promises (superfoods boost immunity) and culturally rooted beliefs (cold foods cause coughs). Despite their widespread influence, the infrastructure for tracing, verifying, and contextualizing these claims remains fragmented and underdeveloped. In this paper, we propose a Food Claim-Traceability Network (FCN) as an extension of FKG[.]in, a knowledge graph of Indian food that we have been incrementally building. We also present the ontology design and the semi-automated knowledge curation workflow that we used to develop a proof of concept of FKG[.]in-FCN using Reddit data and Large Language Models. FCN integrates curated data inputs, structured schemas, and provenance-aware pipelines for food-related claim extraction and validation. While directly linked to the Indian food knowledge graph as an application, our methodology remains application-agnostic and adaptable to other geographic, culinary, or regulatory settings. By modeling food claims and their traceability in a structured, verifiable, and explainable way, we aim to contribute to more transparent and accountable food knowledge ecosystems, supporting researchers, policymakers, and most importantly, everyday consumers in navigating a world saturated with dietary assertions.


The KG-ER Conceptual Schema Language

arXiv.org Artificial Intelligence

We propose KG-ER, a conceptual schema language for knowledge graphs that describes the structure of knowledge graphs independently of their representation (relational databases, property graphs, RDF) while helping to capture the semantics of the information stored in a knowledge graph.


Natural Latents: Latent Variables Stable Across Ontologies

arXiv.org Artificial Intelligence

Suppose two Bayesian agents each learn a generative model of the same environment. We will assume the two have converged on the predictive distribution, i.e. distribution over some observables in the environment, but may have different generative models containing different latent variables. Under what conditions can one agent guarantee that their latents are a function of the other agents latents? We give simple conditions under which such translation is guaranteed to be possible: the natural latent conditions. We also show that, absent further constraints, these are the most general conditions under which translatability is guaranteed. Crucially for practical application, our theorems are robust to approximation error in the natural latent conditions.